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Biol. Unit 1 - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURES OF PHOSPHONOACETAMIDE LIGATED T AND PHOSPHONOACETAMIDE AND MALONATE LIGATED R STATES OF ASPARTATE CARBAMOYLTRANSFERASE AT 2.8-ANGSTROMS RESOLUTION AND NEUTRAL PH

Authors :   J. E. Gouaux, W. N. Lipscomb

Date :   22 Sep 89 (Deposition) - 15 Oct 90 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D  (3x)

Keywords :   Transferase (Carbamoyl-P, Aspartate) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. E. Gouaux, W. N. Lipscomb
Crystal Structures Of Phosphonoacetamide Ligated T And Phosphonoacetamide And Malonate Ligated R States Of Aspartate Carbamoyltransferase At 2. 8-A Resolution And Neutral Ph.
Biochemistry V. 29 389 1990
PubMed-ID: 2405902 | Reference-DOI: 10.1021/BI00454A013
(for further references see the PDB file header)

Molecule 1 - ASPARTATE CARBAMOYLTRANSFERASE (R STATE), CATALYTIC CHAIN
	Chains	:	A, C
	EC Number	:	2.1.3.2
	Engineered	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

Molecule 2 - ASPARTATE CARBAMOYLTRANSFERASE REGULATORY CHAIN
	Chains	:	B, D
	Engineered	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (3x)	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 6)

No.	Name	Count	Type	Full Name
1	MAL	2	Ligand/Ion	MALTOSE
2	PCT	2	Ligand/Ion	PHOSPHONOACETAMIDE
3	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 12)

No.	Name	Count	Type	Full Name
1	MAL	6	Ligand/Ion	MALTOSE
2	PCT	6	Ligand/Ion	PHOSPHONOACETAMIDE
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LYS A:84 , ARG A:167 , THR A:168 , ARG A:229 , GLN A:231 , LEU A:267 , PCT A:311	BINDING SITE FOR RESIDUE MAL A 312
02	AC2	SOFTWARE	LYS C:84 , ARG C:105 , ARG C:167 , THR C:168 , ARG C:229 , GLN C:231 , LEU C:267 , PRO C:268 , PCT C:311	BINDING SITE FOR RESIDUE MAL C 312
03	AC3	SOFTWARE	CYS B:109 , CYS B:114 , CYS B:138 , CYS B:141	BINDING SITE FOR RESIDUE ZN B 154
04	AC4	SOFTWARE	CYS D:109 , CYS D:114 , CYS D:138 , CYS D:141	BINDING SITE FOR RESIDUE ZN D 154
05	AC5	SOFTWARE	SER A:52 , THR A:53 , ARG A:54 , THR A:55 , SER A:80 , LYS A:84 , ARG A:105 , HIS A:134 , GLN A:137 , PRO A:266 , LEU A:267 , MAL A:312	BINDING SITE FOR RESIDUE PCT A 311
06	AC6	SOFTWARE	SER C:52 , THR C:53 , ARG C:54 , THR C:55 , SER C:80 , LYS C:84 , ARG C:105 , HIS C:134 , GLN C:137 , PRO C:266 , LEU C:267 , MAL C:312	BINDING SITE FOR RESIDUE PCT C 311
07	PMA	AUTHOR	ARG A:54 , THR A:55 , ARG A:105 , HIS A:134 , GLN A:137 , ARG A:167 , ARG A:229 , GLN A:231 , PRO A:266 , LEU A:267	BINDING SITES OF COMBINED PCT AND MAL MOLECULES. SITE ACTUALLY CONTAIN AN ADDITIONAL TWO RESIDUES OF SYMMETRY RELATED. THE OTHER RESIDUES, SER A 80, AND LYS A 84 ARE IN AN ADJACENT (THREE-FOLD RELATED) CATALYTIC CHAIN.
08	PMC	AUTHOR	ARG C:54 , THR C:55 , ARG C:105 , HIS C:134 , GLN C:137 , ARG C:167 , ARG C:229 , GLN C:231 , PRO C:266 , LEU C:267	BINDING SITES OF COMBINED PCT AND MAL MOLECULES. SITE ACTUALLY CONTAIN AN ADDITIONAL TWO RESIDUES OF SYMMETRY RELATED. THE OTHER RESIDUES, SER A 80, AND LYS A 84 ARE IN AN ADJACENT (THREE-FOLD RELATED) CATALYTIC CHAIN.
09	ZNB	AUTHOR	CYS B:109 , CYS B:114 , CYS B:138 , CYS B:141	zn binding site
10	ZND	AUTHOR	CYS D:109 , CYS D:114 , CYS D:138 , CYS D:141	zn binding site

(no "SS Bond" information available for 2AT1)

Asymmetric Unit

No.	Residues
1	Leu A:267	-	Pro A:268
2	Leu C:267	-	Pro C:268

(no "SAP(SNP)/Variant" information available for 2AT1)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CARBAMOYLTRANSFERASE	PS00097	Aspartate and ornithine carbamoyltransferases signature.	PYRB_ECOLI	49-56	2	A:48-55 C:48-55

Biological Unit 1 (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CARBAMOYLTRANSFERASE	PS00097	Aspartate and ornithine carbamoyltransferases signature.	PYRB_ECOLI	49-56	6	A:48-55 C:48-55

(no "Exon" information available for 2AT1)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:310
 aligned with PYRB_ECOLI | P0A786 from UniProtKB/Swiss-Prot  Length:311

    Alignment length:310
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311
           PYRB_ECOLI     2 ANPLYQKHIISINDLSRDDLNLVLATAAKLKANPQPELLKHKVIASCFFEASTRTRLSFETSMHRLGASVVGFSDSANTSLGKKGETLADTISVISTYVDAIVMRHPQEGAARLATEFSGNVPVLNAGDGSNQHPTQTLLDLFTIQETQGRLDNLHVAMVGDLKYGRTVHSLTQALAKFDGNRFYFIAPDALAMPQYILDMLDEKGIAWSLHSSIEEVMAEVDILYMTRVQKERLDPSEYANVKAQFVLRASDLHNAKANMKVLHPLPRVDEIATDVDKTPHAWYFQQAGNGIFARQALLALVLNRDLVL 311
               SCOP domains d2at1a1 A:1-150 Aspartate carbamoyltransferase catalytic subunit                                                                                      d2at1a2 A:151-310 Aspartate carbamoyltransferase catalytic subunit                                                                                               SCOP domains
               CATH domains 2at1A01 A:1-133,A:292-310  [code=3.40.50.1370, no name defined]                                                                      2at1A02 A:134-291  [code=3.40.50.1370, no name defined]                                                                                                       2at1A01             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee.......hhhhhhhhhhhhhhhh.........eeeeeee....hhhhhhhhhhhhhh.eeeeeee..............hhhhhhhhhhh.eeeeee....hhhhhhhhh...eeeee.......hhhhhhhhhhhhhhh.....eeeeee......hhhhhhhhhhhhh..eeeeeee.......hhhhhhhhhh..eeeee..hhhhhh...eeeeeee....................hhhhhh.....eeee.........hhhhh.eee.hhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------CARBAMOY--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2at1 A   1 ANPLYQKHIISINDLSRDDLNLVLATAAKLKANPQPELLKHKVIASCFFEASTRTRLSFQTSMHRLGASVVGFSDSANTSLGKKGETLADTISVISTYVDAIVMRHPQEGAARLATEFSGNVPVLNAGDGSNQHPTQTLLDLFTIQQTEGRLDNLHVAMVGDLKYGRTVHSLTQALAKFDGNRFYFIAPDALAMPEYILDMLDEKGIAWSLHSSIEEVMAEVDILYMTRVQKERLDPSEYANVKAQFVLRASDLHNAKANMKVLHPLPRVDEIATDVDKTPHAWYFQQAGNGIFARQALLALVLNRDLVL 310
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310

Chain B from PDB  Type:PROTEIN  Length:146
 aligned with PYRI_ECOLI | P0A7F3 from UniProtKB/Swiss-Prot  Length:153

    Alignment length:146
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147      
           PYRI_ECOLI     8 QVEAIKRGTVIDHIPAQIGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLSEDQVDQLALYAPQATVNRIDNYEVVGKSRPSLPERIDNVLVCPNSNCISHAEPVSSSFAVRKRANDIALKCKYCEKEFSHNVVLAN 153
               SCOP domains d2at1b1 B:8-100 Aspartate carbamoyltransferase                                               d2at1b2 B:101-153                                     SCOP domains
               CATH domains 2at1B01 B:8-100  [code=3.30.70.140, no name defined]                                         2at1B02 B:101-153  [code=2.30.30.20, no name defined] CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee.....hhhhhhhhh.......eeeeee........eeeeeeee......hhhhhhhhh....eeeeee.....eeeee...eeee..................eeeeeee....eeeee....eeeehhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2at1 B   8 GVEAIKRGTVIDHIPAQIGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLSEDQVDQLALYAPQATVNRIDNYEVVGKSRPSLPERIDNVLVCPNSNCISHAEPVSSSFAVRKRANDIALKCKYCEKEFSHNVVLAN 153
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147

Chain C from PDB  Type:PROTEIN  Length:310
 aligned with PYRB_ECOLI | P0A786 from UniProtKB/Swiss-Prot  Length:311

    Alignment length:310
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311
           PYRB_ECOLI     2 ANPLYQKHIISINDLSRDDLNLVLATAAKLKANPQPELLKHKVIASCFFEASTRTRLSFETSMHRLGASVVGFSDSANTSLGKKGETLADTISVISTYVDAIVMRHPQEGAARLATEFSGNVPVLNAGDGSNQHPTQTLLDLFTIQETQGRLDNLHVAMVGDLKYGRTVHSLTQALAKFDGNRFYFIAPDALAMPQYILDMLDEKGIAWSLHSSIEEVMAEVDILYMTRVQKERLDPSEYANVKAQFVLRASDLHNAKANMKVLHPLPRVDEIATDVDKTPHAWYFQQAGNGIFARQALLALVLNRDLVL 311
               SCOP domains d2at1c1 C:1-150 Aspartate carbamoyltransferase catalytic subunit                                                                                      d2at1c2 C:151-310 Aspartate carbamoyltransferase catalytic subunit                                                                                               SCOP domains
               CATH domains 2at1C01 C:1-133,C:292-310  [code=3.40.50.1370, no name defined]                                                                      2at1C02 C:134-291  [code=3.40.50.1370, no name defined]                                                                                                       2at1C01             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee.......hhhhhhhhhhhhhhhh.........eeeeeee....hhhhhhhhhhhhhh.eeeeeee..............hhhhhhhhhhh.eeeeee....hhhhhhhhh...eeeee.......hhhhhhhhhhhhhhh.....eeeeee......hhhhhhhhhhhhh..eeeeeee.......hhhhhhhhhh..eeeee..hhhhhh...eeeeeee....................hhhhhh.....eeee.........hhhhh.eee.hhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------CARBAMOY--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2at1 C   1 ANPLYQKHIISINDLSRDDLNLVLATAAKLKANPQPELLKHKVIASCFFEASTRTRLSFQTSMHRLGASVVGFSDSANTSLGKKGETLADTISVISTYVDAIVMRHPQEGAARLATEFSGNVPVLNAGDGSNQHPTQTLLDLFTIQQTEGRLDNLHVAMVGDLKYGRTVHSLTQALAKFDGNRFYFIAPDALAMPEYILDMLDEKGIAWSLHSSIEEVMAEVDILYMTRVQKERLDPSEYANVKAQFVLRASDLHNAKANMKVLHPLPRVDEIATDVDKTPHAWYFQQAGNGIFARQALLALVLNRDLVL 310
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310

Chain D from PDB  Type:PROTEIN  Length:146
 aligned with PYRI_ECOLI | P0A7F3 from UniProtKB/Swiss-Prot  Length:153

    Alignment length:146
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147      
           PYRI_ECOLI     8 QVEAIKRGTVIDHIPAQIGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLSEDQVDQLALYAPQATVNRIDNYEVVGKSRPSLPERIDNVLVCPNSNCISHAEPVSSSFAVRKRANDIALKCKYCEKEFSHNVVLAN 153
               SCOP domains d2at1d1 D:8-100 Aspartate carbamoyltransferase                                               d2at1d2 D:101-153                                     SCOP domains
               CATH domains 2at1D01 D:8-100  [code=3.30.70.140, no name defined]                                         2at1D02 D:101-153  [code=2.30.30.20, no name defined] CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee.....hhhhhhhhh.......eeeeee........eeeeeeee......hhhhhhhhh....eeeeee.....eeeee...eeee..................eeeeeee....eeeee....eeeehhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2at1 D   8 GVEAIKRGTVIDHIPAQIGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLSEDQVDQLALYAPQATVNRIDNYEVVGKSRPSLPERIDNVLVCPNSNCISHAEPVSSSFAVRKRANDIALKCKYCEKEFSHNVVLAN 153
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Alpha-Beta Plaits (1688)

Homologous Superfamily: [code=3.30.70.140, no name defined] (53)

Escherichia coli. Organism_taxid: 562. (19)

1a	2at1B01	B:8-100
1b	2at1D01	D:8-100

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.1370, no name defined] (91)

Escherichia coli. Organism_taxid: 562. (19)

2a	2at1A02	A:134-291
2b	2at1C02	C:134-291
2c	2at1A01	A:1-133,A:292-310
2d	2at1C01	C:1-133,C:292-310

Class: Mainly Beta (13760)

Architecture: Roll (1513)

Topology: SH3 type barrels. (648)

Homologous Superfamily: [code=2.30.30.20, no name defined] (53)

Escherichia coli. Organism_taxid: 562. (19)

3a	2at1B02	B:101-153
3b	2at1D02	D:101-153

(no "Pfam Domain" information available for 2AT1)

Asymmetric Unit(hide GO term definitions)

Chain A,C (PYRB_ECOLI | P0A786)

molecular function
	GO:0016597	amino acid binding	Interacting selectively and non-covalently with an amino acid, organic acids containing one or more amino substituents.
	GO:0004070	aspartate carbamoyltransferase activity	Catalysis of the reaction: L-aspartate + carbamoyl phosphate = N-carbamoyl-L-aspartate + H(+) + phosphate.
	GO:0016743	carboxyl- or carbamoyltransferase activity	Catalysis of the transfer of a carboxyl- or carbamoyl group from one compound (donor) to another (acceptor).
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0044205	'de novo' UMP biosynthetic process	The chemical reactions and pathways resulting in the formation of UMP, uridine monophosphate, starting with the synthesis of (S)-dihydroorotate from bicarbonate; UMP biosynthesis may either occur via reduction by quinone, NAD(+) or oxygen.
	GO:0006207	'de novo' pyrimidine nucleobase biosynthetic process	The chemical reactions and pathways resulting in the formation of pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases, beginning with the synthesis of a pyrimidine ring from simpler precursors.
	GO:0006520	cellular amino acid metabolic process	The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells.
	GO:0006221	pyrimidine nucleotide biosynthetic process	The chemical reactions and pathways resulting in the formation of a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
	GO:0009220	pyrimidine ribonucleotide biosynthetic process	The chemical reactions and pathways resulting in the formation of a pyrimidine ribonucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
	GO:0000050	urea cycle	The sequence of reactions by which arginine is synthesized from ornithine, then cleaved to yield urea and regenerate ornithine. The overall reaction equation is NH3 + CO2 + aspartate + 3 ATP + 2 H2O = urea + fumarate + 2 ADP + 2 phosphate + AMP + diphosphate.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Chain B,D (PYRI_ECOLI | P0A7F3)

molecular function
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0006207	'de novo' pyrimidine nucleobase biosynthetic process	The chemical reactions and pathways resulting in the formation of pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases, beginning with the synthesis of a pyrimidine ring from simpler precursors.
	GO:0006221	pyrimidine nucleotide biosynthetic process	The chemical reactions and pathways resulting in the formation of a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
cellular component
	GO:0009347	aspartate carbamoyltransferase complex	A multienzyme complex that catalyzes the formation N-carbamoyl-L-aspartate from carbamoyl phosphate and L-aspartate. It exhibits a variety of architectural organizations, but in all microorganisms the core catalytic component is a homotrimer of approximately 34 kDa polypeptides.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
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	2at1
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(no "Related Entries Specified in the PDB File" available for 2AT1)

Description

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Ligands, Modified Residues, Ions (3, 6)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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Exons (0, 0)

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